Link to MOD pages

[svenmh]

Can somebody go through the organisms at:

https://github.com/svenmh/BioGRID-Viewer/blob/master/BGV/taxa.json

and git a list of mod links for me?

[RoseO]

I asked Bobby-Joe to send the MOD links since he probably has them all available. Just a minor point --- you have A. thaliana listed twice in your list (taxa.json).

[svenmh]

A. thaliana now only listed once, thanks!

[svenmh]

Got a list of links from Bobby-Joe, for some either the tab2 files does not seem to have the correct id to link to those genes or they are buried in the "Synonyms/Aliases" column.

BAD: zfin, flip, mgi,rgd,tair,xenbase

OK: Yeast, Worm, ecoli,maize

so I think we are going to have to forget getting all the links before August.

[RoseO]

That's too bad. Maybe if you forward his email with the MOD link info, I can take a look at the broken links and see if I can help out. For example, MGI is linked from BioGRID pages. I know there was a broken link before, but now there seems to be a redirect, e.g. :

the MGI link in the external databases list on this page:

http://thebiogrid.org/200416/table/mus-musculus/hras1.html

goes to:

http://www.informatics.jax.org/marker/MGI:96224

Maybe I can help out if I can see what you're working with.

On Jul 9, 2012, at 3:51 PM, Sven Heinicke wrote:

Got a list of links from Bobby-Joe, for some either the tab2 files does not seem to have the correct id to link to those genes or they are buried in the "Synonyms/Aliases" column.

BAD: zfin, flip, mgi,rgd,tair,xenbase

OK: Yeast, Worm, ecoli,maize

so I think we are going to have to forget getting all the links before August.

---

Reply to this email directly or view it on GitHub: https://github.com/svenmh/BioGRID-Viewer/issues/41#issuecomment-6857557

[svenmh]

the issue with mouse is that the tab2 does not have MGI numbers. I think I could link it to:

http://www.informatics.jax.org/searchtool/Search.do?query=hras1

and let the human pick.

[RoseO]

It's possible that you might need two fields that are not in the tab2 file, i.e. : external_ids and external_types (external databases)

What did Bobby-Joe send you, only the URL parameters?

On Jul 10, 2012, at 9:14 AM, Sven Heinicke wrote:

the issue with mouse is that the tab2 does not have MGI numbers. I think I could like it to:

http://www.informatics.jax.org/searchtool/Search.do?query=hras1

and let the human pick.

---

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[svenmh]

Long term, after August, I think I'm going to have to abandon the tab2 format perhaps for psi25 format (which is more complicated, bigger, less redundant, and has MGI number) or more directly access BioGRID database format rather then have me reimplement another BioGRID database.

I just hope I get access to a real BioGRID dev system soon so I don't have to code like I'm not a part of the group. Enclosed in the first bit of code I've seen from BioGRID that isn't mine. It's what Bobby-Joe sent me about the links. (also, lets see if Github can handle attachments, if not I'll send it directly.)

[RoseO]

No attachment through GitHub. Please send it directly. Thanks!

On Jul 10, 2012, at 9:48 AM, Sven Heinicke wrote:

Long term, after August, I think I'm going to have to abandon the tab2 format perhaps for psi25 format (which is more complicated, bigger, less redundant, and has MGI number) or more directly access BioGRID database format rather then have me reimplement another BioGRID database.

I just hope I get access to a real BioGRID dev system soon so I don't have to code like I'm not a part of the group. Enclosed in the first bit of code I've seen from BioGRID that isn't mine. It's what Bobby-Joe sent me about the links. (also, lets see if Github can handle attachments, if not I'll send it directly.)

---

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[RoseO]

Yeah, from the script that Bobby-Joe sent to you, it looks like it requires the external_id and external_type fields from the database that aren't in the tab2 file:

... fetchExternalLinks( $idList, $idTypeList, $organismOfficialName ) {

    $idList = explode( "|", $idList );
    $idTypeList = explode( "|", $idTypeList );

...

On Jul 10, 2012, at 9:48 AM, Sven Heinicke wrote:

Long term, after August, I think I'm going to have to abandon the tab2 format perhaps for psi25 format (which is more complicated, bigger, less redundant, and has MGI number) or more directly access BioGRID database format rather then have me reimplement another BioGRID database.

I just hope I get access to a real BioGRID dev system soon so I don't have to code like I'm not a part of the group. Enclosed in the first bit of code I've seen from BioGRID that isn't mine. It's what Bobby-Joe sent me about the links. (also, lets see if Github can handle attachments, if not I'll send it directly.)

---

Reply to this email directly or view it on GitHub: https://github.com/svenmh/BioGRID-Viewer/issues/41#issuecomment-6875896

[RoseO]

Or maybe they're called "external_ids_types"

$externalLinkouts = self::fetchExternalLinks( $annotationInfo->external_ids, $annotationInfo->external_ids_types, $annotationInfo->organism_official_name );

On Jul 10, 2012, at 9:58 AM, Rose Oughtred wrote:

Yeah, from the script that Bobby-Joe sent to you, it looks like it requires the external_id and external_type fields from the database that aren't in the tab2 file:

... fetchExternalLinks( $idList, $idTypeList, $organismOfficialName ) {

  $idList = explode( "|", $idList );
  $idTypeList = explode( "|", $idTypeList );

...

On Jul 10, 2012, at 9:48 AM, Sven Heinicke wrote:

Long term, after August, I think I'm going to have to abandon the tab2 format perhaps for psi25 format (which is more complicated, bigger, less redundant, and has MGI number) or more directly access BioGRID database format rather then have me reimplement another BioGRID database.

I just hope I get access to a real BioGRID dev system soon so I don't have to code like I'm not a part of the group. Enclosed in the first bit of code I've seen from BioGRID that isn't mine. It's what Bobby-Joe sent me about the links. (also, lets see if Github can handle attachments, if not I'll send it directly.)

---

Reply to this email directly or view it on GitHub: https://github.com/svenmh/BioGRID-Viewer/issues/41#issuecomment-6875896

[svenmh]

I think this is a conversation for after the yeast meeting. I'd be uncomfortable changing the data format before the yeast meeting.

[RoseO]

Okay. Let me know if I can be of any help with this after the meeting.

On Jul 10, 2012, at 10:05 AM, Sven Heinicke wrote:

I think this is a conversation for after the yeast meeting. I'd be uncomfortable changing the data format before the yeast meeting.

---

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[svenmh]

The stuff I'm showing at today's meeting required no special access to BioGRID data. I even gave up using the BioGRID rest server. If I continue to get the support I've been getting there is no way this will be integrated in BioGRID within the next 20 day.

[RoseO]

I understand. Hope it all gets sorted out sooner rather than later.

On Jul 10, 2012, at 10:14 AM, Sven Heinicke wrote:

The stuff I'm showing at today's meeting required no special access to BioGRID data. I even gave up using the BioGRID rest server. If I continue to get the support I've been getting there is no way this will be integrated in BioGRID within the next 20 day.

---

Reply to this email directly or view it on GitHub: https://github.com/svenmh/BioGRID-Viewer/issues/41#issuecomment-6876666